Pathogens constitute a critical problem for human, animal and plant health. Pathogens may cause infections that result in a variety of human illnesses and can lead to a large number of deaths. Such pathogens may include viruses, bacteria, prions, fungi, molds, eukaryotic microbes and parasites of many types. Moreover, pathogens infect agriculturally important plant and animal species, resulting in economic hardship. Detection and identification of pathogens in relevant materials (e.g., water, air, blood, tissues, organs, etc.) is essential to minimize the transfer and spread of infections. Furthermore, quick identification may aid in devising effective treatment strategies.
One class of pathogens is viruses. Viruses are used here as an example and not intended to limit the scope of the invention in any way. Viral infections extol a great morbidity and mortality among the human population. Many of these infections result from undetected viruses in waters, foods and air and are promulgated by an ever-increasing interconnection of societies. Detection and identification in medically-important materials such as blood, blood derivatives, tissues and organs is critical to minimize potentials for transfer and spread within hospitals and clinics and to the staff of these centers.
Several popular methods for the detection and identification of viruses and pathogens exist. These generally fall into three categories: A) Infectivity and infectivity reduction assays; B) Serology assays employing antibody detection to determine whether an individual has been exposed; and C) Direct virology assays in which antibodies are used to detect the presence of an antigen in the sample or nucleic acid-based assays in which elements of the viral genome are detected. Infectivity-based assays are seldom used in diagnostics yet, both cell culture and animal-based amplification of virus in a sample may be necessary for many of the current diagnostic procedures. The use of animals in infectivity assays is costly, time consuming and subject to ethical dispute. Serodiagnosis still exists in many-hospitals principally because there are no good alternatives for some infections. Serology is largely performed to determine antibody levels and to estimate the probability for infection. Antibody based tests are popular, but are usually limited to a battery of individual tests in a macroscopic format (e.g., Enzyme Linked ImmunoSorbant Assay, or ELISA). Standard microbiological approaches to detect anthrax and other bacterial pathogens involve growth of the agent on nutrient agar and visual identification after various staining procedures. Carbon source utilization testing in various media identifies and differentiates among closely related isolates. Viral pathogens are usually identified after their administration, infection and amplification in animals, particularly embryonated eggs, mice or cell culture. This is the basic microbial identification scheme practiced today. While precise in their verification of pathogen identity, these procedures are very slow.
False-positives and false-negatives, particularly in cases where there is known cross reaction with antigens produced by other infections, are of major importance. Polymerase chain reaction (PCR) tests are extremely sensitive and are usually employed in cases where there is prior reason to suspect the presence of a particular pathogen, such as following a positive test for HIV antigens. PCR methods, however, are relatively costly and time consuming. Furthermore, PCR tests are of a relatively limited applicability because of the requirement of enzyme activity and because of the frequency of false positives.